If your flashplugin only recognizes the very first mouse click and then seems to ignore the mouse completely, just click somewhere outside the area where the flash script is (e.g. on the webpage background) and then flash will recognize the next click.

Some more promising solutions are these:

• ubuntugeek.com: edit the file
  /usr/lib/nspluginwrapper/i386/linux/npviewer and add the following line just before the last one:
  export GDK_NATIVE_WINDOWS=1
  The complete file should now look somewhat like this:
  #!/bin/sh
TARGET_OS=linux
TARGET_ARCH=i386
export GDK_NATIVE_WINDOWS=1
. /usr/lib/nspluginwrapper/noarch/npviewer
• if you are on a 64bit machine, install the 64bit flashplugin from this PPA

Flash Preferences unusable

If your clicks onto the Flash preferences are not recognized, close gnome-do and/or docky. After that, the preferences should be clickable again. (found here)